VarDict: adjust filtering for 1.4.9 release
VarDict: adjust filtering for 1.4.9 release

Latest release avoids double counting overlapping fragments but
requires a slight adjustment in post-call quality score filtering
for low depth reads. This improves sensitivity and specificity in
validations against the DREAM synthetic 4 dataset:

http://imgur.com/a/SF2a8
https://github.com/AstraZeneca-NGS/VarDictJava/issues/60#issuecomment-276657197

lbeltrame/bcbio-nextgen,lbeltrame/bcbio-nextgen,chapmanb/bcbio-nextgen,vladsaveliev/bcbio-nextgen,lbeltrame/bcbio-nextgen,a113n/bcbio-nextgen,biocyberman/bcbio-nextgen,chapmanb/bcbio-nextgen,biocyberman/bcbio-nextgen,vladsaveliev/bcbio-nextgen,vladsaveliev/bcbio-nextgen,a113n/bcbio-nextgen,biocyberman/bcbio-nextgen,chapmanb/bcbio-nextgen,a113n/bcbio-nextgen